id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16745	Warning when mmCIF metric table used for an AlphaFold 3 ligand	goddard@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202501142332 (2025-01-14 23:32:44 UTC)
Description
A recent update to Google's AlphaFold3 puts per-residue pLDDT scores in the _ma_qa_metric_local mmCIF table.  In this example with a protein chain A and two small molecule ligands with chain ids B and C opening the mmCIF gives a  warning about ""No chain in structure corresponds to chain ID given in local score info (chain 'B')"".  Maybe it should assign the score to the specified ligand residue even though it is not a polymer.  But maybe not since I see from the file that the ligand does not even have residue numbers and the metric table lists the residue number as ""."" for chain B and the atom_site table also gives the chain B residue numbers as ""."".

If it can easily be made to assign the residue attribute that would be nice since users could then color by attribute using AlphaFold pLDDT and it would correctly color the ligands too, not just the polymer chains.

I've attached the offending AlphaFold 3 mmCIF file.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.10.dev202501142332 (2025-01-14)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/goddard/ucsf/data/alphafold3/wynton_nipah_zmr/8xps_a_zmr_jan30/8xps_a_zmr_jan30_model.cif
> format mmcif

Chain information for 8xps_a_zmr_jan30_model.cif #1  
---  
Chain | Description  
A | .  
  

No chain in structure corresponds to chain ID given in local score info (chain
'B')  

Computing secondary structure  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.8.0, Qt 6.8.1
Qt runtime version: 6.8.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac Studio
      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
      Total Number of Cores: 24 (16 performance and 8 efficiency)
      Memory: 64 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 14 days, 17 minutes

Graphics/Displays:

    Apple M2 Ultra:

      Chipset Model: Apple M2 Ultra
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 60
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        PHL 278B1:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
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    anyio: 4.8.0
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    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
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    ChimeraX-UI: 1.43
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
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File attachment: 8xps_a_zmr_jan30_model.cif
}}}

[attachment:""8xps_a_zmr_jan30_model.cif""]
"	defect	accepted	moderate		Input/Output								all	ChimeraX